[2024-01-24 13:41:10,439] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,441] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,441] [INFO] DQC Reference Directory: /var/lib/cwl/stg70c43e55-3012-4b93-87cd-d7f03a9a704f/dqc_reference
[2024-01-24 13:41:11,798] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:11,799] [INFO] Task started: Prodigal
[2024-01-24 13:41:11,799] [INFO] Running command: gunzip -c /var/lib/cwl/stg56f36f1f-0580-4aa3-9858-d3955f6954e2/GCF_902726545.1_IP42281v1_genomic.fna.gz | prodigal -d GCF_902726545.1_IP42281v1_genomic.fna/cds.fna -a GCF_902726545.1_IP42281v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:23,211] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:23,211] [INFO] Task started: HMMsearch
[2024-01-24 13:41:23,211] [INFO] Running command: hmmsearch --tblout GCF_902726545.1_IP42281v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70c43e55-3012-4b93-87cd-d7f03a9a704f/dqc_reference/reference_markers.hmm GCF_902726545.1_IP42281v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:23,515] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:23,516] [INFO] Found 6/6 markers.
[2024-01-24 13:41:23,567] [INFO] Query marker FASTA was written to GCF_902726545.1_IP42281v1_genomic.fna/markers.fasta
[2024-01-24 13:41:23,567] [INFO] Task started: Blastn
[2024-01-24 13:41:23,568] [INFO] Running command: blastn -query GCF_902726545.1_IP42281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70c43e55-3012-4b93-87cd-d7f03a9a704f/dqc_reference/reference_markers.fasta -out GCF_902726545.1_IP42281v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:24,361] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:24,364] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:24,364] [INFO] Target genome list was writen to GCF_902726545.1_IP42281v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:24,368] [INFO] Task started: fastANI
[2024-01-24 13:41:24,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg56f36f1f-0580-4aa3-9858-d3955f6954e2/GCF_902726545.1_IP42281v1_genomic.fna.gz --refList GCF_902726545.1_IP42281v1_genomic.fna/target_genomes.txt --output GCF_902726545.1_IP42281v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:38,340] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:38,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70c43e55-3012-4b93-87cd-d7f03a9a704f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:38,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70c43e55-3012-4b93-87cd-d7f03a9a704f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:38,351] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:38,351] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:38,351] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Yersinia artesiana	strain=IP42281	GCA_902726545.1	2890315	2890315	type	True	100.0	1414	1420	95	conclusive
Yersinia proxima	strain=IP37424	GCA_902170785.1	2890316	2890316	type	True	94.6842	1279	1420	95	below_threshold
Yersinia enterocolitica subsp. enterocolitica	strain=NBRC 105693	GCA_001598735.1	150052	630	type	True	93.9036	1223	1420	95	below_threshold
Yersinia enterocolitica subsp. enterocolitica	strain=NCTC12982	GCA_901472495.1	150052	630	type	True	93.8874	1228	1420	95	below_threshold
Yersinia enterocolitica	strain=ATCC 9610	GCA_000755055.1	630	630	type	True	93.8593	1238	1420	95	below_threshold
Yersinia enterocolitica subsp. palearctica	strain=NCTC13769	GCA_900637005.1	150053	630	type	True	93.7899	1195	1420	95	below_threshold
Yersinia enterocolitica subsp. palearctica	strain=Y11	GCA_000253175.1	150053	630	type	True	93.7518	1200	1420	95	below_threshold
Yersinia alsatica	strain=IP38850	GCA_902170305.1	2890317	2890317	type	True	85.9461	1138	1420	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	85.6426	1022	1420	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.2427	374	1420	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.1934	409	1420	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.125	395	1420	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	78.7891	378	1420	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:38,354] [INFO] DFAST Taxonomy check result was written to GCF_902726545.1_IP42281v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:38,355] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:38,355] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:38,356] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70c43e55-3012-4b93-87cd-d7f03a9a704f/dqc_reference/checkm_data
[2024-01-24 13:41:38,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:38,406] [INFO] Task started: CheckM
[2024-01-24 13:41:38,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902726545.1_IP42281v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902726545.1_IP42281v1_genomic.fna/checkm_input GCF_902726545.1_IP42281v1_genomic.fna/checkm_result
[2024-01-24 13:42:15,847] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:15,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:15,867] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:15,867] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:15,867] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902726545.1_IP42281v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:15,868] [INFO] Task started: Blastn
[2024-01-24 13:42:15,868] [INFO] Running command: blastn -query GCF_902726545.1_IP42281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70c43e55-3012-4b93-87cd-d7f03a9a704f/dqc_reference/reference_markers_gtdb.fasta -out GCF_902726545.1_IP42281v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:16,815] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:16,818] [INFO] Selected 13 target genomes.
[2024-01-24 13:42:16,819] [INFO] Target genome list was writen to GCF_902726545.1_IP42281v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:16,865] [INFO] Task started: fastANI
[2024-01-24 13:42:16,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg56f36f1f-0580-4aa3-9858-d3955f6954e2/GCF_902726545.1_IP42281v1_genomic.fna.gz --refList GCF_902726545.1_IP42281v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902726545.1_IP42281v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:29,335] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:29,348] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:29,348] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_902726525.1	s__Yersinia enterocolitica_H	99.9673	1399	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.97	99.97	0.99	0.99	3	conclusive
GCF_001995075.1	s__Yersinia enterocolitica_F	94.6894	1289	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.25	99.14	0.94	0.92	3	-
GCF_901472495.1	s__Yersinia enterocolitica	93.8716	1229	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	97.11	96.22	0.89	0.83	185	-
GCF_900460525.1	s__Yersinia kristensenii	88.1504	1147	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.20	97.89	0.92	0.89	22	-
GCF_003600645.1	s__Yersinia rochesterensis	88.0742	1135	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.46	98.81	0.94	0.91	13	-
GCF_009831415.1	s__Yersinia canariae	87.857	1180	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.93	98.81	0.93	0.92	3	-
GCF_004124235.1	s__Yersinia hibernica	86.5497	1162	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.98	98.46	0.91	0.87	4	-
GCF_001098625.1	s__Yersinia frederiksenii_C	85.8911	1150	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.63	97.69	0.93	0.89	21	-
GCF_000173735.1	s__Yersinia aldovae	85.7479	990	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.00	96.65	0.94	0.91	11	-
GCF_000754805.1	s__Yersinia frederiksenii	85.5915	1131	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.36	98.91	0.95	0.85	11	-
GCF_001152565.1	s__Yersinia pekkanenii	84.824	1015	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.90	99.90	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:29,350] [INFO] GTDB search result was written to GCF_902726545.1_IP42281v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:29,350] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:29,353] [INFO] DFAST_QC result json was written to GCF_902726545.1_IP42281v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:29,354] [INFO] DFAST_QC completed!
[2024-01-24 13:42:29,354] [INFO] Total running time: 0h1m19s